Online Resource 2. SSRs markers characteristics

Article title: Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity; a perspective for genetic association studies.

Journal name: Molecular Genetics and Genomics

Author names: A. García-Lor1, F. Luro2, L. Navarro1 and P. Ollitrault1,3

Affiliation: 1 Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain; 2 Unité de recherche GEQA, Institut National de la Recherche Agronomique (INRA), 20230 San Giuliano, France; 3 International Center for of Agricultural Research for Development (CIRAD), Department BIOS, TGU AGAP, Avenue Agropolis, TA A-75/02. F-34398 Montpellier Cedex 5, France

Corresponding authors:

Patrick Ollitrault. International Center for of Agricultural Research for Development (CIRAD), Department BIOS, TGU AGAP, Avenue Agropolis, TA A-75/02. F-34398 Montpellier Cedex 5, France. Email:

Luis Navarro. Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain. Email:

LG / Pos / Marker name / Reverse sequence / Forward sequence / AT / Size / EMBL
Accession / Published / Motif
1 / 58 / MEST121 / TCCCTATCATCGGCAACTTC / CAATAATGTTAGGCTGGATGGA / 55 / 177-189 / DY275927 / Luro et al. 2008
1 / 71 / MEST1 / CAAGCCTCTCTCTTTAGTCCCA / AGTTCTTTGGTGCTTCAGGC / 55 / 170-190 / DY262452 / New primer / (TC)14
1 / 90 / MEST431 / GAGCTCAAAACAATAGCCGC / CATACCTCCCCGTCCATCTA / 55 / 331-345 / DY291553 / New primer / (CAG)7
1 / 120 / TAA15 / GAAAGGGTTACTTGACCAGGC / CTTCCCAGCTGCACAAGC / 55 / 164-204 / Kijas et al. 1997
2 / 13 / mCrCIR02D09 / AATGATGAGGGTAAAGATG / ACCCATCACAAAACAGA / 55 / 226-240 / FR677569 / Cuenca et al. 2011
2 / 28 / mCrCIR04H06 / GGACATAGTGAGAAGTTGG / CAAAGTGGTGAAACCTG / 55 / 184-196 / FR677579 / Cuenca et al. 2011
2 / 53 / CAC15 / TAAATCTCCACTCTGCAAAAGC / GATAGGAAGCGTCGTAGACCC / 55 / 168-180 / Kijas et al. 1997
2 / 99 / mCrCIR03C08 / CAGAGACAGCCAAGAGA / GCTTCTTACATTCCTCAAA / 55 / 200-225 / FR677576 / Cuenca et al. 2011
2 / 148 / MEST46 / GAACCAGAATCAGAACCCGA / GGTGAGCATCTGGACGACTT / 55 / 230-256 / DY266487 / New primer / (CAA)7
2 / 153 / mCrCIR05A05 / CGGAACAACTAAAACAAT / TGGGCTTGTAGACAGTTA / 50 / 144-179 / FR677580 / Cuenca et al. 2011
2 / 154 / mCrCI01C07 / GTCACTCACTCTCGCTCTTG / TTGCTAGCTGCTTTAACTTT / 55 / 260-298 / AJ567394 / Froelicher et al. 2008
2 / 161 / TAA41 / AGGTCTACATTGGCATTGTC / ACATGCAGTGCTATAATGAATG / 55 / 127-162 / Kijas et al. 1997
2 / 162 / mCrCIR06B07 / CGGAACAACTAAAACAAT / TGGGCTTGTAGACAGTTA / 50 / 96-108 / AM489745 / Froelicher et al. 2008
3 / 17 / MEST256 / CATTAAAATATCCGTGCCGC / GAGCAAGTGCGTTGTTGTGT / 55 / 200-230 / DY290355 / New primer / (TAT)8
3 / 179 / MEST131 / TACCTCCACGTGTCAAACCA / GCTGTCACGTTGGGTGTATG / 55 / 120-150 / DY276912 / New primer / (GCCCCA)5
4 / 16 / mCrCIR07D06 / CCTTTTCACAGTTTGCTAT / TCAATTCCTCTAGTGTGTGT / 55 / 164-197 / FR677581 / Cuenca et al. 2011
4 / 75 / mCrCIR03G05 / CCACACAGGCAGACA / CCTTGGAGGAGCTTTAC / 50 / 199-228 / FR677578 / Cuenca et al. 2011
4 / 86 / mCrCI02D04b / CTCTCTTTCCCCATTAGA / AGCAAACCCCACAAC / 50 / 199-229 / FR677564 / Kamiri et al. 2011
4 / 90 / mCrCI03D12a / GCCATAAGCCCTTTCT / CCCACAACCATCACC / 50 / 240-280 / FR677577 / Aleza et al. 2011
5 / 16 / MEST15 / TTATTACGAAGCGGAGGTGG / GCCTCGCATTCTCTTGACTC / 55 / 192-210 / FC912829 / New primer / (GAG)6
5 / 23 / mCrCIR01F08a / ATGAGCTAAAGAGAAGAGG / GGACTCAACACAACACAA / 50 / 128-156 / AM489737 / Froelicher et al. 2008
5 / 35 / MEST104 / CCTTATCTTCATCACCTCCGTC / TAAAAAGATGGGGCCTTGTG / 55 / 240-260 / DY273697 / New primer / (TC)15, (CT)6
5 / 53 / mCrCI05A04 / AAACGAGACAAGACCAAC / TATCAAACTCCCCTCACT / 55 / 245-268 / FR692372 / Froelicher com pers
5 / 57 / MEST88 / GCCTGTTTGCTTTCTCTTTCTC / ATGAGAGCCAAGAGCACGAT / 55 / 99-130 / DY271576 / New primer / (TC)7
5 / 93 / mCrCIR06A12 / CCCAACAAACTCAAACTTC / TTTTTATTTCGGTCTCCTT / 50 / 84-102 / AM489742 / Froelicher et al. 2008
5 / 95 / mCrCIR07E12 / TGTAGTCAAAAGCATCAC / TCTATGATTCCTGACTTTA / 50 / 106-146 / AM489750 / Froelicher et al. 2008
5 / 96 / MEST115 / CCCCCTCTTCTTTCACACAA / GGTGAGCAGCCATCTTCTTC / 55 / 147-167 / DY274953 / New primer / (GA)7
5 / 105 / MEST56 / AGTCCGCCTTTGCTTTTTCT / GGTGCAAAAGAGAGCGAGAG / 55 / 129-145 / DY267791 / Aleza et al. (2011)
6 / 2 / mCrCI04H12 / TTCCTCTACAACTACAACCA / ATTATCCTCAACCTCCAA / 50 / 179-194 / FR692371 / Froelicher com pers
6 / 61 / mCrCIR02F12 / GGCCATTTCTCTGATG / TAACTGAGGGATTGGTTT / 55 / 116-144 / FR677570 / Cuenca et al. 2011
6 / 65 / MEST192 / CGCGGATCATCTAGCATACA / CTTGGCACCATCAACACATC / 55 / 200-240 / DY283129 / Aleza et al (2011)
6 / 67 / Ci01D11 / GCAAAACAAGCAGACTACAAAT / AGGACAGATGACCCAGATGACA / 55 / 214-230 / AJ567397 / Froelicher et al. 2008
6 / 68 / MEST488 / CACGCTCTTGACTTTCTCCC / CTTTGCGTGTTTGTGCTGTT / 55 / 133-164 / DY297637 / New primer / (CT)21
6 / 71 / mCrCIR01E02 / TGAATGGTACGGGAAATGC / CAGGGTCGGTGGAGAGGAT / 55 / 172-184 / AM489735 / Froelicher et al. 2008
6 / 89 / mCrCIR01C06 / GGACCACAACAAAGACAG / TGGAGACACAAAGAAGAA / 50 / 131-170 / AJ567393 / Cuenca et al. 2011
6 / 93 / TAA1 / GACAACATCAACAACAGCAAGAGC / AAGAAGAAGAGCCCCCATTAGC / 55 / 161-180 / Kijas et al. 1997
7 / 9 / MEST107 / GCTGAGATGGGGATGAAAGA / CCCCATCCTTTCAACTTGTG / 55 / 183-201 / DY274062 / New primer / (AGA)6
7 / 83 / mCrCIR03B07 / CACCTTTCCCTTCCA / TGAGGGACTAAACAGCA / 55 / 263-279 / FR677573 / Cuenca et al. 2011
7 / 98 / Ci07C07 / TATCCAGTTTGTAAATGAG / TGATATTTGATTAGTTTGG / 50 / 243-258 / AJ567409 / Froelicher et al. 2008
8 / 6 / mCrCIR01F04a / AAGCATTTAGGGAGGGTCACT / TGCTGCTGCTGTTGTTGTTCT / 55 / 190-228 / AM489736 / Froelicher et al. 2008
8 / 15 / MEST86 / CCAACTGACACTAATCCTCTTCC / CCTCTCTGGCTTCTGGATTG / 55 / 110-128 / DY271447 / New primer / (GTC)6
8 / 33 / mCrCIR07B05 / TTTGTTCTTTTTGGTCTTTT / CTTTTCTTTCCTAGTTTCCC / 50 / 218-254 / AM489747 / Froelicher et al. 2008
8 / 56 / Ci02F07 / GCAGCGTTTGTTTTCT / TGCTGGTTTTCAGATACTT / 55 / 188-215 / AJ567406 / Froelicher et al. 2008
8 / 58 / mCrCIR02G02 / CAATAAGAAAACGCAGG / TGGTAGAGAAACAGAGGTG / 55 / 110-138 / FR677572 / Cuenca et al. 2011
8 / 98 / mCrCIR02A09 / ACAGAAGGTAGTATTTTAGGG / TTGTTTGGATGGGAAG / 55 / 151-177 / FR677568 / Cuenca et al. 2011
9 / 0 / Ci02B07 / CAGCTCAACATGAAAGG / TTGGAGAACAGGATGG / 50 / 178-212 / AJ567403 / Froelicher et al. 2008
9 / 49 / mCrCIR07F11 / ACTATGATTACTTTGCTTTGAG / GAAGAAACAAGAAAAAAAAAT / 50 / 146-176 / FR677567 / Kamiri et al. 2011
- / - / CAC23 / ATCACAATTACTAGCAGCGCC / TTGCATTGTAGCATGTTGG / 55 / 240-260 / Kijas et al. 1997
- / - / mCrCI02G12 / AAACCGAAATACAAGAGTG / TCCACAAACAATACAACG / 55 / 240-260 / FR677575 / Froelicher com pers
- / - / Ci07C09 / GACCCTGCCTCCAAAGTATC / GTGGCTGTTGAGGGGTTG / 55 / 258-274 / AJ567410 / Froelicher et al. 2008

(LG) Linkage group; (Pos) Position genetic map, centimorgans (cM); (AT) Annealing Temperature ºC

LG and position from Ollitrault P, Terol J, Chen C, Federici CT, Lofty S, Hippolyte I, Ollitrault F, Berard A, Chauveau A, Constantino G, Kacar Y, Mu L, Cuenca J, Garcia-Lor A, Froelicher Y, Aleza P, Boland A, Billot C, Navarro L, Luro F, Roose ML, Gmitter FG, Talon M, Brunel D (2011) A Reference Linkage Map Of C. clementina Based On SNPs, SSRs And Indels. Plant & Animal Genomes XIX Conference. San Diego, CA (USA) P477